BiDiBlast pipeline

BiDiBlast specifications

Information


Unique identifier OMICS_13938
Name BiDiBlast
Alternative name Bi-Directional BLAST
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java, Perl
License GNU General Public License version 2.0
Computer skills Medium
Stability Stable
Maintained Yes

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Documentation


Publication for Bi-Directional BLAST

BiDiBlast IN pipelines

 (5)
2016
PMCID: 4831748
PMID: 27077738
DOI: 10.1371/journal.pone.0152943

[…] by rt-qpcr experiments., aspecies and accession number of the genes that were used as reference sequences for the tblastx search., bbest hits of the olive transcripts, as identified using a bi-directional blast search., ce-value of the best hit identified by the blastx search., *transcripts selected for the rt-qpcr analyses., the differential expression of the most interesting genes […]

2014
PMCID: 3948071
PMID: 24571091
DOI: 10.1186/1471-2164-15-164

[…] m. roreri had 7,060,129 bases associated with repeats and repetitive elements while m. perniciosa had 1,737,865 bases associated with repeats and repetitive elements (additional file 1)., using a bi-directional blast with an e-value of e-04 as the cut-off value for two proteins being considered a match, a whole genome comparison of the predicted proteins between the m. roreri and m. […]

2014
PMCID: 4105132
PMID: 25000941
DOI: 10.1186/1756-3305-7-314

[…] to compare with these four translated genomes using blastx (e-value < = 1e-5), and sequences producing significant alignments were calculated and kept for further analysis. secondly, to conduct bi-directional blast, we then performed a reciprocal search with tblastn (e-value < = 1e-5) using these 4 dipteran genomes as the queries, respectively. the top hit sequence was determined […]

2013
PMCID: 4054855
PMID: 23800011
DOI: 10.1186/gb-2013-14-6-r64

[…] 0.5 mbp, shift size 0.1 mbp) to define synteny by the density of homology matches between query and reference genome., the corresponding orthologous genes were anchored to the marker backbone via bi-directional blast hits. genes without marker association were located according to their position in the corresponding reference genomes. the obtained 1bl linear ordered gene map was then expanded […]

2008
PMCID: 2483987
PMID: 18598343
DOI: 10.1186/1471-2164-9-318

[…] required to use the go annotation of the arabidopsis proteins to the corresponding citrus gene. a hmmer search [55] was also done to identify putative pfam domains [25] in the unigenes. finally, a bi-directional blast comparison was also performed with arabidopsis protein database to obtain a set of putative orthologs. in these analyses, two sequences were considered orthologs when each one […]

BiDiBlast institution(s)
Centro de Recursos Microbiológicos (CREM), Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal

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